Other useful methods


In this section, you can learn useful methods but not in other sections.

Table of contents

  • Get Network from cytosacpe

    • Cytoscape.js
    • NetworkX
    • DataFrame
    • igraph
  • Select

    • edges
    • nodes
  • Hide

    • edges
    • nodes
  • Clear Selection


In [ ]:

Prepare network data



In [6]:
# import data from url
from py2cytoscape.data.cyrest_client import CyRestClient
from IPython.display import Image
import json

# Create REST client for Cytoscape
cy = CyRestClient()

# Reset current session for fresh start
cy.session.delete()

# Load a sample network
network = cy.network.create_from('http://chianti.ucsd.edu/~kono/data/galFiltered.sif')

# Apply layout to the cytoscape network object
cy.layout.apply(network = network)

# Show it!!
Image(network.get_png(height=400))


Out[6]:

Get Network from Cytoscape


You can get network data in the following forms:

  • Cytoscape.js
  • NetworkX
  • DataFrame
  • igraph

As Cytoscape.js



In [15]:
# As Cytoscape.js (dict)
network_json = network.to_json()

print(json.dumps(network_json, indent=4))


{
    "data": {
        "__Annotations": [],
        "name": "galFiltered.sif",
        "SUID": 12778,
        "shared_name": "galFiltered.sif",
        "selected": true
    },
    "format_version": "1.0",
    "target_cytoscapejs_version": "~2.1",
    "elements": {
        "edges": [
            {
                "data": {
                    "name": "YDR277C (pp) YDL194W",
                    "SUID": 13479,
                    "shared_interaction": "pp",
                    "source": "13476",
                    "id": "13479",
                    "interaction": "pp",
                    "target": "13478",
                    "shared_name": "YDR277C (pp) YDL194W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YDR277C (pp) YJR022W",
                    "SUID": 13477,
                    "shared_interaction": "pp",
                    "source": "13476",
                    "id": "13477",
                    "interaction": "pp",
                    "target": "12836",
                    "shared_name": "YDR277C (pp) YJR022W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YPR145W (pp) YMR117C",
                    "SUID": 13471,
                    "shared_interaction": "pp",
                    "source": "13470",
                    "id": "13471",
                    "interaction": "pp",
                    "target": "13419",
                    "shared_name": "YPR145W (pp) YMR117C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YER054C (pp) YBR045C",
                    "SUID": 13469,
                    "shared_interaction": "pp",
                    "source": "13467",
                    "id": "13469",
                    "interaction": "pp",
                    "target": "13464",
                    "shared_name": "YER054C (pp) YBR045C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YER054C (pp) YER133W",
                    "SUID": 13468,
                    "shared_interaction": "pp",
                    "source": "13467",
                    "id": "13468",
                    "interaction": "pp",
                    "target": "13179",
                    "shared_name": "YER054C (pp) YER133W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YBR045C (pp) YOR178C",
                    "SUID": 13466,
                    "shared_interaction": "pp",
                    "source": "13464",
                    "id": "13466",
                    "interaction": "pp",
                    "target": "13181",
                    "shared_name": "YBR045C (pp) YOR178C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YBR045C (pp) YIL045W",
                    "SUID": 13465,
                    "shared_interaction": "pp",
                    "source": "13464",
                    "id": "13465",
                    "interaction": "pp",
                    "target": "13364",
                    "shared_name": "YBR045C (pp) YIL045W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YBL079W (pp) YDL088C",
                    "SUID": 13463,
                    "shared_interaction": "pp",
                    "source": "13462",
                    "id": "13463",
                    "interaction": "pp",
                    "target": "13429",
                    "shared_name": "YBL079W (pp) YDL088C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YLR345W (pp) YLR321C",
                    "SUID": 13461,
                    "shared_interaction": "pp",
                    "source": "13460",
                    "id": "13461",
                    "interaction": "pp",
                    "target": "13125",
                    "shared_name": "YLR345W (pp) YLR321C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YGR136W (pp) YGR058W",
                    "SUID": 13445,
                    "shared_interaction": "pp",
                    "source": "13444",
                    "id": "13445",
                    "interaction": "pp",
                    "target": "12983",
                    "shared_name": "YGR136W (pp) YGR058W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YDL023C (pp) YJL159W",
                    "SUID": 13443,
                    "shared_interaction": "pp",
                    "source": "13442",
                    "id": "13443",
                    "interaction": "pp",
                    "target": "13015",
                    "shared_name": "YDL023C (pp) YJL159W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YBR170C (pp) YGR048W",
                    "SUID": 13439,
                    "shared_interaction": "pp",
                    "source": "13438",
                    "id": "13439",
                    "interaction": "pp",
                    "target": "13169",
                    "shared_name": "YBR170C (pp) YGR048W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YGR074W (pp) YBR043C",
                    "SUID": 13475,
                    "shared_interaction": "pp",
                    "source": "13435",
                    "id": "13475",
                    "interaction": "pp",
                    "target": "13474",
                    "shared_name": "YGR074W (pp) YBR043C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YGL202W (pp) YGR074W",
                    "SUID": 13436,
                    "shared_interaction": "pp",
                    "source": "13434",
                    "id": "13436",
                    "interaction": "pp",
                    "target": "13435",
                    "shared_name": "YGL202W (pp) YGR074W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YLR197W (pp) YOR310C",
                    "SUID": 13433,
                    "shared_interaction": "pp",
                    "source": "13431",
                    "id": "13433",
                    "interaction": "pp",
                    "target": "12904",
                    "shared_name": "YLR197W (pp) YOR310C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YLR197W (pp) YDL014W",
                    "SUID": 13432,
                    "shared_interaction": "pp",
                    "source": "13431",
                    "id": "13432",
                    "interaction": "pp",
                    "target": "12903",
                    "shared_name": "YLR197W (pp) YDL014W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YDL088C (pp) YER110C",
                    "SUID": 13430,
                    "shared_interaction": "pp",
                    "source": "13429",
                    "id": "13430",
                    "interaction": "pp",
                    "target": "13256",
                    "shared_name": "YDL088C (pp) YER110C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YMR117C (pp) YPR010C",
                    "SUID": 13422,
                    "shared_interaction": "pp",
                    "source": "13419",
                    "id": "13422",
                    "interaction": "pp",
                    "target": "13421",
                    "shared_name": "YMR117C (pp) YPR010C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YMR117C (pp) YCL032W",
                    "SUID": 13420,
                    "shared_interaction": "pp",
                    "source": "13419",
                    "id": "13420",
                    "interaction": "pp",
                    "target": "12939",
                    "shared_name": "YMR117C (pp) YCL032W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YML114C (pp) YDR167W",
                    "SUID": 13418,
                    "shared_interaction": "pp",
                    "source": "13417",
                    "id": "13418",
                    "interaction": "pp",
                    "target": "13271",
                    "shared_name": "YML114C (pp) YDR167W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YNL036W (pp) YIR009W",
                    "SUID": 13416,
                    "shared_interaction": "pp",
                    "source": "13415",
                    "id": "13416",
                    "interaction": "pp",
                    "target": "12961",
                    "shared_name": "YNL036W (pp) YIR009W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YOR212W (pp) YLR362W",
                    "SUID": 13440,
                    "shared_interaction": "pp",
                    "source": "13413",
                    "id": "13440",
                    "interaction": "pp",
                    "target": "12942",
                    "shared_name": "YOR212W (pp) YLR362W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YDR070C (pp) YFL017C",
                    "SUID": 13411,
                    "shared_interaction": "pp",
                    "source": "13410",
                    "id": "13411",
                    "interaction": "pp",
                    "target": "12806",
                    "shared_name": "YDR070C (pp) YFL017C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YGR046W (pp) YNL236W",
                    "SUID": 13402,
                    "shared_interaction": "pp",
                    "source": "13401",
                    "id": "13402",
                    "interaction": "pp",
                    "target": "12970",
                    "shared_name": "YGR046W (pp) YNL236W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YIL070C (pp) YML054C",
                    "SUID": 13396,
                    "shared_interaction": "pp",
                    "source": "13395",
                    "id": "13396",
                    "interaction": "pp",
                    "target": "12989",
                    "shared_name": "YIL070C (pp) YML054C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YPR113W (pd) YMR043W",
                    "SUID": 13394,
                    "shared_interaction": "pd",
                    "source": "13393",
                    "id": "13394",
                    "interaction": "pd",
                    "target": "13012",
                    "shared_name": "YPR113W (pd) YMR043W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YER081W (pp) YIL074C",
                    "SUID": 13392,
                    "shared_interaction": "pp",
                    "source": "13391",
                    "id": "13392",
                    "interaction": "pp",
                    "target": "13349",
                    "shared_name": "YER081W (pp) YIL074C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YGR088W (pd) YLR256W",
                    "SUID": 13390,
                    "shared_interaction": "pd",
                    "source": "13389",
                    "id": "13390",
                    "interaction": "pd",
                    "target": "12988",
                    "shared_name": "YGR088W (pd) YLR256W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YDR395W (pp) YPR102C",
                    "SUID": 13459,
                    "shared_interaction": "pp",
                    "source": "13386",
                    "id": "13459",
                    "interaction": "pp",
                    "target": "13305",
                    "shared_name": "YDR395W (pp) YPR102C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YDR395W (pp) YOL127W",
                    "SUID": 13458,
                    "shared_interaction": "pp",
                    "source": "13386",
                    "id": "13458",
                    "interaction": "pp",
                    "target": "12880",
                    "shared_name": "YDR395W (pp) YOL127W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YDR395W (pp) YIL052C",
                    "SUID": 13457,
                    "shared_interaction": "pp",
                    "source": "13386",
                    "id": "13457",
                    "interaction": "pp",
                    "target": "13456",
                    "shared_name": "YDR395W (pp) YIL052C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YDR395W (pp) YER056CA",
                    "SUID": 13455,
                    "shared_interaction": "pp",
                    "source": "13386",
                    "id": "13455",
                    "interaction": "pp",
                    "target": "13454",
                    "shared_name": "YDR395W (pp) YER056CA",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YDR395W (pp) YNL069C",
                    "SUID": 13453,
                    "shared_interaction": "pp",
                    "source": "13386",
                    "id": "13453",
                    "interaction": "pp",
                    "target": "13452",
                    "shared_name": "YDR395W (pp) YNL069C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YDR395W (pp) YIL133C",
                    "SUID": 13451,
                    "shared_interaction": "pp",
                    "source": "13386",
                    "id": "13451",
                    "interaction": "pp",
                    "target": "12861",
                    "shared_name": "YDR395W (pp) YIL133C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YDR395W (pp) YDL075W",
                    "SUID": 13450,
                    "shared_interaction": "pp",
                    "source": "13386",
                    "id": "13450",
                    "interaction": "pp",
                    "target": "13449",
                    "shared_name": "YDR395W (pp) YDL075W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YGR085C (pp) YDR395W",
                    "SUID": 13387,
                    "shared_interaction": "pp",
                    "source": "13384",
                    "id": "13387",
                    "interaction": "pp",
                    "target": "13386",
                    "shared_name": "YGR085C (pp) YDR395W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YGR085C (pp) YLR075W",
                    "SUID": 13385,
                    "shared_interaction": "pp",
                    "source": "13384",
                    "id": "13385",
                    "interaction": "pp",
                    "target": "13304",
                    "shared_name": "YGR085C (pp) YLR075W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YDL030W (pp) YMR005W",
                    "SUID": 13376,
                    "shared_interaction": "pp",
                    "source": "13373",
                    "id": "13376",
                    "interaction": "pp",
                    "target": "13375",
                    "shared_name": "YDL030W (pp) YMR005W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YDL030W (pp) YDL013W",
                    "SUID": 13374,
                    "shared_interaction": "pp",
                    "source": "13373",
                    "id": "13374",
                    "interaction": "pp",
                    "target": "12849",
                    "shared_name": "YDL030W (pp) YDL013W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YER079W (pp) YNL154C",
                    "SUID": 13372,
                    "shared_interaction": "pp",
                    "source": "13370",
                    "id": "13372",
                    "interaction": "pp",
                    "target": "13098",
                    "shared_name": "YER079W (pp) YNL154C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YER079W (pp) YHR135C",
                    "SUID": 13371,
                    "shared_interaction": "pp",
                    "source": "13370",
                    "id": "13371",
                    "interaction": "pp",
                    "target": "13093",
                    "shared_name": "YER079W (pp) YHR135C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YDL215C (pp) YLR432W",
                    "SUID": 13369,
                    "shared_interaction": "pp",
                    "source": "13367",
                    "id": "13369",
                    "interaction": "pp",
                    "target": "13272",
                    "shared_name": "YDL215C (pp) YLR432W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YDL215C (pd) YER040W",
                    "SUID": 13368,
                    "shared_interaction": "pd",
                    "source": "13367",
                    "id": "13368",
                    "interaction": "pd",
                    "target": "13056",
                    "shared_name": "YDL215C (pd) YER040W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YPR041W (pp) YMR309C",
                    "SUID": 13360,
                    "shared_interaction": "pp",
                    "source": "13358",
                    "id": "13360",
                    "interaction": "pp",
                    "target": "12913",
                    "shared_name": "YPR041W (pp) YMR309C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YPR041W (pp) YOR361C",
                    "SUID": 13359,
                    "shared_interaction": "pp",
                    "source": "13358",
                    "id": "13359",
                    "interaction": "pp",
                    "target": "12912",
                    "shared_name": "YPR041W (pp) YOR361C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YOR120W (pd) YPL248C",
                    "SUID": 13357,
                    "shared_interaction": "pd",
                    "source": "13356",
                    "id": "13357",
                    "interaction": "pd",
                    "target": "12957",
                    "shared_name": "YOR120W (pd) YPL248C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YIL074C (pp) YNL311C",
                    "SUID": 13350,
                    "shared_interaction": "pp",
                    "source": "13349",
                    "id": "13350",
                    "interaction": "pp",
                    "target": "13143",
                    "shared_name": "YIL074C (pp) YNL311C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YDR299W (pd) YJL194W",
                    "SUID": 13348,
                    "shared_interaction": "pd",
                    "source": "13347",
                    "id": "13348",
                    "interaction": "pd",
                    "target": "13330",
                    "shared_name": "YDR299W (pd) YJL194W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YHR005C (pp) YLR362W",
                    "SUID": 13409,
                    "shared_interaction": "pp",
                    "source": "13345",
                    "id": "13409",
                    "interaction": "pp",
                    "target": "12942",
                    "shared_name": "YHR005C (pp) YLR362W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YLR452C (pp) YHR005C",
                    "SUID": 13346,
                    "shared_interaction": "pp",
                    "source": "13344",
                    "id": "13346",
                    "interaction": "pp",
                    "target": "13345",
                    "shared_name": "YLR452C (pp) YHR005C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YMR255W (pp) YGL122C",
                    "SUID": 13363,
                    "shared_interaction": "pp",
                    "source": "13342",
                    "id": "13363",
                    "interaction": "pp",
                    "target": "12789",
                    "shared_name": "YMR255W (pp) YGL122C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YBR274W (pp) YMR255W",
                    "SUID": 13343,
                    "shared_interaction": "pp",
                    "source": "13341",
                    "id": "13343",
                    "interaction": "pp",
                    "target": "13342",
                    "shared_name": "YBR274W (pp) YMR255W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YHR084W (pd) YFL026W",
                    "SUID": 13383,
                    "shared_interaction": "pd",
                    "source": "13339",
                    "id": "13383",
                    "interaction": "pd",
                    "target": "13027",
                    "shared_name": "YHR084W (pd) YFL026W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YHR084W (pd) YDR461W",
                    "SUID": 13382,
                    "shared_interaction": "pd",
                    "source": "13339",
                    "id": "13382",
                    "interaction": "pd",
                    "target": "13021",
                    "shared_name": "YHR084W (pd) YDR461W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YHR084W (pp) YMR043W",
                    "SUID": 13381,
                    "shared_interaction": "pp",
                    "source": "13339",
                    "id": "13381",
                    "interaction": "pp",
                    "target": "13012",
                    "shared_name": "YHR084W (pp) YMR043W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YBL050W (pp) YOR036W",
                    "SUID": 13337,
                    "shared_interaction": "pp",
                    "source": "13336",
                    "id": "13337",
                    "interaction": "pp",
                    "target": "13052",
                    "shared_name": "YBL050W (pp) YOR036W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YBL026W (pp) YOR167C",
                    "SUID": 13480,
                    "shared_interaction": "pp",
                    "source": "13334",
                    "id": "13480",
                    "interaction": "pp",
                    "target": "12834",
                    "shared_name": "YBL026W (pp) YOR167C",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YJL194W (pd) YMR043W",
                    "SUID": 13331,
                    "shared_interaction": "pd",
                    "source": "13330",
                    "id": "13331",
                    "interaction": "pd",
                    "target": "13012",
                    "shared_name": "YJL194W (pd) YMR043W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YLR258W (pp) YBR274W",
                    "SUID": 13366,
                    "shared_interaction": "pp",
                    "source": "13328",
                    "id": "13366",
                    "interaction": "pp",
                    "target": "13341",
                    "shared_name": "YLR258W (pp) YBR274W",
                    "selected": false
                }
            },
            {
                "data": {
                    "name": "YLR258W (pp) YIL045W",
                    "SUID": 13365,
                    "shared_interaction": "pp",
                    "source": "13328",
                    "id": "13365",
                    "interaction": "pp",
                    "target": "13364",
                    "shared_name": "YLR258W (pp) YIL045W",
                    "selected": false
                }
            },
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                    "shared_name": "YEL009C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12920",
                    "name": "YBR155W",
                    "SUID": 12920,
                    "shared_name": "YBR155W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12919",
                    "name": "YMR186W",
                    "SUID": 12919,
                    "shared_name": "YMR186W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12917",
                    "name": "YGL106W",
                    "SUID": 12917,
                    "shared_name": "YGL106W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12916",
                    "name": "YOR326W",
                    "SUID": 12916,
                    "shared_name": "YOR326W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12913",
                    "name": "YMR309C",
                    "SUID": 12913,
                    "shared_name": "YMR309C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12912",
                    "name": "YOR361C",
                    "SUID": 12912,
                    "shared_name": "YOR361C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12910",
                    "name": "YIL105C",
                    "SUID": 12910,
                    "shared_name": "YIL105C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12908",
                    "name": "YLR134W",
                    "SUID": 12908,
                    "shared_name": "YLR134W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12906",
                    "name": "YER179W",
                    "SUID": 12906,
                    "shared_name": "YER179W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12904",
                    "name": "YOR310C",
                    "SUID": 12904,
                    "shared_name": "YOR310C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12903",
                    "name": "YDL014W",
                    "SUID": 12903,
                    "shared_name": "YDL014W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12901",
                    "name": "YPR119W",
                    "SUID": 12901,
                    "shared_name": "YPR119W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12899",
                    "name": "YLR117C",
                    "SUID": 12899,
                    "shared_name": "YLR117C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12897",
                    "name": "YGL013C",
                    "SUID": 12897,
                    "shared_name": "YGL013C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12895",
                    "name": "YCR086W",
                    "SUID": 12895,
                    "shared_name": "YCR086W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12894",
                    "name": "YDR412W",
                    "SUID": 12894,
                    "shared_name": "YDR412W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12892",
                    "name": "YPL201C",
                    "SUID": 12892,
                    "shared_name": "YPL201C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12891",
                    "name": "YER062C",
                    "SUID": 12891,
                    "shared_name": "YER062C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12889",
                    "name": "YOR327C",
                    "SUID": 12889,
                    "shared_name": "YOR327C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12887",
                    "name": "YER143W",
                    "SUID": 12887,
                    "shared_name": "YER143W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12886",
                    "name": "YAL030W",
                    "SUID": 12886,
                    "shared_name": "YAL030W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12884",
                    "name": "YOL086C",
                    "SUID": 12884,
                    "shared_name": "YOL086C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12882",
                    "name": "YDR050C",
                    "SUID": 12882,
                    "shared_name": "YDR050C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12880",
                    "name": "YOL127W",
                    "SUID": 12880,
                    "shared_name": "YOL127W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12877",
                    "name": "YIL069C",
                    "SUID": 12877,
                    "shared_name": "YIL069C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12875",
                    "name": "YER074W",
                    "SUID": 12875,
                    "shared_name": "YER074W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12873",
                    "name": "YBR093C",
                    "SUID": 12873,
                    "shared_name": "YBR093C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12871",
                    "name": "YDR171W",
                    "SUID": 12871,
                    "shared_name": "YDR171W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12869",
                    "name": "YCL030C",
                    "SUID": 12869,
                    "shared_name": "YCL030C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12867",
                    "name": "YNL301C",
                    "SUID": 12867,
                    "shared_name": "YNL301C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12865",
                    "name": "YOL120C",
                    "SUID": 12865,
                    "shared_name": "YOL120C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12863",
                    "name": "YLR044C",
                    "SUID": 12863,
                    "shared_name": "YLR044C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12861",
                    "name": "YIL133C",
                    "SUID": 12861,
                    "shared_name": "YIL133C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12859",
                    "name": "YHR174W",
                    "SUID": 12859,
                    "shared_name": "YHR174W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12857",
                    "name": "YGR254W",
                    "SUID": 12857,
                    "shared_name": "YGR254W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12855",
                    "name": "YCR012W",
                    "SUID": 12855,
                    "shared_name": "YCR012W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12854",
                    "name": "YNL216W",
                    "SUID": 12854,
                    "shared_name": "YNL216W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12852",
                    "name": "YAL038W",
                    "SUID": 12852,
                    "shared_name": "YAL038W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12851",
                    "name": "YNL307C",
                    "SUID": 12851,
                    "shared_name": "YNL307C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12849",
                    "name": "YDL013W",
                    "SUID": 12849,
                    "shared_name": "YDL013W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12848",
                    "name": "YER116C",
                    "SUID": 12848,
                    "shared_name": "YER116C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12846",
                    "name": "YNR053C",
                    "SUID": 12846,
                    "shared_name": "YNR053C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12844",
                    "name": "YLR264W",
                    "SUID": 12844,
                    "shared_name": "YLR264W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12841",
                    "name": "YEL015W",
                    "SUID": 12841,
                    "shared_name": "YEL015W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12839",
                    "name": "YNL050C",
                    "SUID": 12839,
                    "shared_name": "YNL050C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12837",
                    "name": "YNR050C",
                    "SUID": 12837,
                    "shared_name": "YNR050C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12836",
                    "name": "YJR022W",
                    "SUID": 12836,
                    "shared_name": "YJR022W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12834",
                    "name": "YOR167C",
                    "SUID": 12834,
                    "shared_name": "YOR167C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12833",
                    "name": "YER112W",
                    "SUID": 12833,
                    "shared_name": "YER112W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12831",
                    "name": "YCL067C",
                    "SUID": 12831,
                    "shared_name": "YCL067C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12829",
                    "name": "YBR112C",
                    "SUID": 12829,
                    "shared_name": "YBR112C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12828",
                    "name": "YCR084C",
                    "SUID": 12828,
                    "shared_name": "YCR084C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12826",
                    "name": "YIL061C",
                    "SUID": 12826,
                    "shared_name": "YIL061C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12825",
                    "name": "YGR203W",
                    "SUID": 12825,
                    "shared_name": "YGR203W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12820",
                    "name": "YJL013C",
                    "SUID": 12820,
                    "shared_name": "YJL013C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12818",
                    "name": "YGL229C",
                    "SUID": 12818,
                    "shared_name": "YGL229C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12817",
                    "name": "YJL030W",
                    "SUID": 12817,
                    "shared_name": "YJL030W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12815",
                    "name": "YGR014W",
                    "SUID": 12815,
                    "shared_name": "YGR014W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12814",
                    "name": "YPL211W",
                    "SUID": 12814,
                    "shared_name": "YPL211W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12812",
                    "name": "YGL044C",
                    "SUID": 12812,
                    "shared_name": "YGL044C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12811",
                    "name": "YOL123W",
                    "SUID": 12811,
                    "shared_name": "YOL123W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12808",
                    "name": "YAL003W",
                    "SUID": 12808,
                    "shared_name": "YAL003W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12806",
                    "name": "YFL017C",
                    "SUID": 12806,
                    "shared_name": "YFL017C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12804",
                    "name": "YDR429C",
                    "SUID": 12804,
                    "shared_name": "YDR429C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12803",
                    "name": "YMR146C",
                    "SUID": 12803,
                    "shared_name": "YMR146C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12801",
                    "name": "YLR293C",
                    "SUID": 12801,
                    "shared_name": "YLR293C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12799",
                    "name": "YBR118W",
                    "SUID": 12799,
                    "shared_name": "YBR118W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12797",
                    "name": "YPR080W",
                    "SUID": 12797,
                    "shared_name": "YPR080W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12796",
                    "name": "YLR249W",
                    "SUID": 12796,
                    "shared_name": "YLR249W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12794",
                    "name": "YOR204W",
                    "SUID": 12794,
                    "shared_name": "YOR204W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12792",
                    "name": "YGL097W",
                    "SUID": 12792,
                    "shared_name": "YGL097W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12791",
                    "name": "YGR218W",
                    "SUID": 12791,
                    "shared_name": "YGR218W",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12789",
                    "name": "YGL122C",
                    "SUID": 12789,
                    "shared_name": "YGL122C",
                    "selected": false
                }
            },
            {
                "data": {
                    "id": "12788",
                    "name": "YKR026C",
                    "SUID": 12788,
                    "shared_name": "YKR026C",
                    "selected": false
                }
            }
        ]
    },
    "generated_by": "cytoscape-3.4.0"
}

As NetworkX



In [16]:
# As NetworkX graph object
network_networkx = network.to_networkx()

num_nodes = network_networkx.number_of_nodes()
num_edges = network_networkx.number_of_edges()

print('Number of Nodes: ' + str(num_nodes))
print('Number of Edges: ' + str(num_edges))


Number of Nodes: 331
Number of Edges: 362

As DataFrame



In [17]:
# As a simple, SIF-like DataFrame
network_df = network.to_dataframe()
network_df.head()


Out[17]:
source interaction target
0 13476 pp 13478
1 13476 pp 12836
2 13470 pp 13419
3 13467 pp 13464
4 13467 pp 13179

As igraph



In [3]:
import py2cytoscape.util.util_igraph as util_ig

# convert cytoscape object to igraph object
network_igraph = util_ig.to_igraph(network.to_json())

Select


You may want to select edges and nodes. By using following methods, you can select edges and nodes and if you would like to select them by attribution, you should read and try this examples.

Select Edges


In [5]:
import pandas as pd
df = pd.DataFrame({
        "name" : ["YKR026C"],
        "selected" : [True]
    }
)
network.update_node_table(df = df, network_key_col = 'name', data_key_col = 'name')


Out[5]:
['Marquee',
 'Sample1',
 'Ripple',
 'Big Labels',
 'Sample2',
 'Curved',
 'default',
 'Universe',
 'Solid',
 'Gradient1',
 'Sample3',
 'default black',
 'Minimal',
 'Directed',
 'Nested Network Style']

Select Nodes


In [7]:
import pandas as pd
df = pd.DataFrame({
        "name" : ["YKR026C"],
        "selected" : [True]
    }
)
network.update_node_table(df = df, network_key_col = 'name', data_key_col = 'name')

In [ ]:

Hide


Hide Edges


In [ ]:

Hide Nodes


In [ ]:

Clear Selection



In [ ]:


In [ ]: